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feed_vmr_table.py
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import sys
import datetime
import re
from psycopg2 import sql
def feed_vmr_table (dict_of_samples,antimicrobian_agent_names_ids,sampleT_terms,isolateT_terms,hostT_terms,sequenceT_terms,repositoryT_terms,riskT_terms,amrT_terms,antiT_terms,environmental_conditions_terms,bioinformatics_terms,taxonomic_information_terms,conn,cursor,new_ont_terms,terms_accepting_multiple_values,sample_flagged_list,mode):
def fix(fields):
fields = fields.replace("\n", "")
fields = fields.replace(" ", "_")
fields = fields.replace("/", "_")
fields = fields.replace("-", "_")
fields = fields.replace("(", "")
fields = fields.replace(")", "")
return(fields)
def getTermAndId (variable):
term=""
id=""
if ("//" in str(variable)):
listF = re.split("//",variable)
#print(listF.groups()[1])
print(listF[0])
term = listF[0]
id = listF[1]
else:
term= variable
return (term,id)
def getTermAndId2 (variable):
term=""
id=""
if ("//" in str(variable)):
listF = re.split("//",variable)
#print(listF.groups()[1])
print(listF[0])
term = listF[0]
id=listF[1]
else:
term= variable
id=None
return (term,id)
def columnIns (column_ins,fields,count,length):
# print ('before',column_ins)
column_ins += fields.upper()
# print ('after',column_ins)
if (count +1 != length):
column_ins += ","
return(column_ins)
def valuesIns (term):
# print ('before',values)
#print ('before',term)
if (term == None):
value = None
else:
value = str(term)
# print ('after',values)
# if (count +1 != length):
# values += ","
return(value)
def check_exists_id(term,field,table):
result=""
if (isinstance(term, list)):
print ("here before LIST",term)
if (table == "alternative_sample_ids") | (table == "alternative_isolate_ids"):
sql_query = """
SELECT *
FROM """ + table + """
WHERE """ + field[0] + """ = %s
AND """ + field[1] + """ = %s;
"""
cursor.execute(sql_query,(term[0],term[1]))
result = cursor.fetchall()
print(result,"come on")
else:
term1 = term[0]
print(term)
#sys.exit()
term2,Oid = getTermAndId(term[1])
print ("here ",term1,term2)
sql_query = """
SELECT *
FROM """ + table + """
WHERE """+field[0]+""" = %s
AND """+field[1]+""" = (SELECT id from """+field[2]+""" where """+field[3].upper()+""" = %s);
"""
print (sql_query,(term1,Oid))
#sys.exit()
cursor.execute(sql_query, (term1, Oid))
result = cursor.fetchall()
print(result,"come on")
if (result):
result = "yes"
else:
result = ""
else:
print ("here WRONGbefore")
##psampling_activity_id = check_exists_id([collection_id,activity],["id","term_id","ontology_terms","ontology_id"],"sample_activity")
term,Oid = getTermAndId(term)
command=""
if (table == "metagenomic_extractions" or table == "wgs_extractions"):
command = "SELECT extraction_id from "+table+" where "+field.upper()+" = %s"
else:
command = "SELECT id from "+table+" where "+field.upper()+" = %s"
print (command,term)
cursor.execute(command,(term,))
result = cursor.fetchone()
print(result,"here")
conn.commit()
print(result, "HERE RESULT OH MY")
return(result)
def check_exists_id2(term,field,table):
result=""
if (isinstance(term, list)):
# print ("here before",term)
term1 = term[0]
term2 = term[1]
print ("here ",term1,term2)
sql_query = """
SELECT *
FROM """ + table + """
WHERE """+field[0]+""" = %s
AND """+field[1]+""" = %s;
"""
print (sql_query,(term2,term1))
cursor.execute(sql_query, (term2, term1))
result = cursor.fetchall()
# print(result,"come on")
if (result):
result = "yes"
else:
result = ""
return(result)
def print_inserts(insert_string,values):
formatted_insert = insert_string
formatted_insert = formatted_insert.replace(" RETURNING id", "")
for term in values:
if term is None:
term_str = 'NULL'
elif isinstance(term, str):
term_str = f"'{term}'"
else:
term_str = str(term)
formatted_insert = formatted_insert.replace('%s', term_str, 1)
output_file = "formatted_sql_command.txt"
with open(output_file, "a") as file: # 'a' mode opens the file for appending
file.write(formatted_insert + ";\n")
def check_controlled_term(term,id,table,field):
print (term,table,field,id)
sql_query = """
SELECT id
FROM {}
WHERE {}=%s
""".format(table, field.upper())
print("SQL Query:", sql_query) # Print the query for debugging
print("Parameter:", (id,)) # Print the parameters for debugging
cursor.execute(sql_query, (id,))
result = cursor.fetchone()
if result is not None:
print("Result ID:", result[0], "Input ID:", id)
else:
print("No result found for ID:", id)
if not result:
print ("Here not result")
sql = ""
if (str(table.upper()) == "MICROBES"):
sql = "INSERT INTO "+str(table.upper())+"(SCIENTIFIC_NAME,"+str(field.upper())+",CURATED) VALUES (%s,%s,%s)"
print_inserts(sql,(term,id,'false'))
print(sql,(term,id,'false'))
cursor.execute(sql,(term,id,'false'))
conn.commit()
else:
sql = "INSERT INTO "+str(table.upper())+"(EN_TERM,"+str(field.upper())+",EN_DESCRIPTION,FR_TERM,FR_DESCRIPTION,CURATED) VALUES (%s,%s,%s,%s,%s,%s)"
description = "Term still not in the vocabulary, added temporary untill solving the problem"
if not id:
id = term
print_inserts(sql,(term,id,description))
print(sql,(term,id,description,'NULL','NULL','false'))
cursor.execute(sql,(term,id,description,'NULL','NULL','false'))
conn.commit()
else:
print (result)
#print("Formatted SQL command:", formatted_insert)
def create_insert (row,fields,controlled_fields,table_name,length):
print (row,fields,controlled_fields, "in create Insert")
#print(length)
#sys.exit()
#AMR_aid =create_insert(dict_of_samples['AMR'][index],AMR_afields,AMR_acontrolled,"amr_antibiotics_profile",len(AMR_afields))
#create_insert({"id":parent_id,"term_id":term},{"id":"id","term_id":"term_id"},{"term_id":["ontology_terms","ontology_id"]},table_multi,2)
column_ins = "("
count=0
values ="("
list_terms = []
for field in fields.keys():
print('lets go first with ', field)
if field in row.keys():
print (row[field],"AQUI TERM O DOIDO VE AQUI!")
terms,id = getTermAndId2(row[field])
#field = fix(field)
# print(fields)
column_ins = columnIns(column_ins,fields[field],count,length)
print (field, controlled_fields, 'COMPARACAO')
if controlled_fields:
if field in controlled_fields.keys():
print (field,'controlled')
list_terms.append(id)
check_controlled_term(terms,id,controlled_fields[field][0],controlled_fields[field][1])
values += "(SELECT id from "+controlled_fields[field][0]+" where "+controlled_fields[field][1].upper()+" = %s)"
if (count +1 != length):
values += ","
else:
print (field,'not controlled')
list_terms.append(valuesIns(terms))
values += "%s"
if (count +1 != length):
values += ","
else:
list_terms.append(valuesIns(terms))
values += "%s"
if (count +1 != length):
values += ","
else:
# print('before2',fields)
# field = fix(field)
# print(fields)
column_ins = columnIns(column_ins,fields[field],count,length)
list_terms.append(valuesIns(None))
values += "%s"
if (count +1 != length):
values += ","
#print(column_ins)
count += 1
#conn.commit()
column_ins += ")"
values += ")"
print (column_ins)
print (values)
#sys.exit()
last_created_id = ""
tables_multi = ["alternative_sample_ids","alternative_isolate_ids","sample_purposes","sample_activities","food_data_product","food_data_product_property","food_data_source", "food_data_packaging","anatomical_data_body","anatomical_data_part","anatomical_data_material","environmental_data_material","environmental_data_site","environmental_data_weather_type","environmental_data_presampling_weather_conditions","environment_data_available_data_type","environmental_data_animal_plant","risk_activity","metagenomic_extractions","wgs_extractions","sequencing_purposes"]
if table_name in tables_multi:
print (table_name,"here multi")
insert = "INSERT INTO "+table_name.upper()+column_ins+" VALUES "+values
print (insert,list_terms)
print_inserts(insert,list_terms)
cursor.execute(insert, list_terms)
conn.commit()
print('inserted with success')
else:
insert = "INSERT INTO "+table_name.upper()+column_ins+" VALUES "+values+" RETURNING id"
print (insert,list_terms)
print_inserts(insert,list_terms)
#f (table_name == 'extractions'):
#print ("look",insert,list_terms)
#sys.exit()
cursor.execute(insert, list_terms)
#print(cursor)
last_created_id = cursor.fetchone()
conn.commit()
print('inserted with success')
return(last_created_id)
#def multi (row,sfield,parent_field,parent_id,tfield,table_field,table_multi):
def multi (row,sfield,parent_field,parent_id,table_multi):
#x x x term_id
###multi(dict_of_samples['sample'][index],"food_product","food_data",food_data_id,"food_product","food_products","food_data_product")
print (row,sfield,parent_field,parent_id,table_multi)
print ('sfield:',sfield)
print ('spield:',parent_field)
print('ddddddddd',parent_id)
if sfield in row.keys():
terms = row[sfield]
if (sfield == 'food_product_properties'):
print (terms)
# print (spurposes)
for term in terms:
#purpose_sampling_id = check_exists_id([collection_id,purpose],["id","term_id","ontology_terms","ontology_id"],"sample_purposes")
id = check_exists_id([parent_id,term],["id","term_id","ontology_terms","ontology_id"],table_multi)
if id != "yes":
print ("doesnt exists")
#purpose_sampling_id =create_insert({"id":collection_id,"term_id":purpose},{"id":"id","term_id":"term_id"},{"term_id":["ontology_terms","ontology_id"]},"sample_purposes",2)
create_insert({"id":parent_id,"term_id":term},{"id":"id","term_id":"term_id"},{"term_id":["ontology_terms","ontology_id"]},table_multi,2)
#print ('DONE???HERE')
else:
print (parent_field,"exists and ",term," exists.")
def extraction_insert(table):
#extraction_id = check_exists_id(dict_of_samples['sample'][index]["sample_id"],"sample_id","extraction_information")
extraction_id = ""
extraction_fields = {
'experimental_protocol_field':'experimental_protocol_field',
'experimental_specimen_role_type':'experimental_specimen_role_type',
"nucleic_acid_extraction_method":"nucleic_acid_extraction_method",
"nucleic_acid_extraction_kit":"nucleic_acid_extraction_kit",
"sample_volume_measurement_value":"sample_volume_measurement_value",
"sample_volume_measurement_unit":"sample_volume_measurement_unit",
"residual_sample_status":"residual_sample_status",
"sample_storage_duration_value":"sample_storage_duration_value",
"sample_storage_duration_unit":"sample_storage_duration_unit",
"nucleic_acid_storage_duration_value":"nucleic_acid_storage_duration_value",
"nucleic_acid_storage_duration_unit":"nucleic_acid_storage_duration_unit"
}
extraction_controlled_fields = {
'experimental_specimen_role_type':["ontology_terms","ontology_id"],
'sample_volume_meaturement_unit':["ontology_terms","ontology_id"],
'residual_sample_status':["ontology_terms","ontology_id"],
'sample_storage_duration_unit':["ontology_terms","ontology_id"],
'nucleic_acid_storage_duration_unit':["ontology_terms","ontology_id"]
}
extraction_id =create_insert(table,extraction_fields,extraction_controlled_fields,"extractions",len(extraction_fields))
return(extraction_id)
#print(dict_of_samples['sample'][index].keys())
host_country={}
#print ("size is ",len(dict_of_samples['sample']))
#sys.exit()
for index in dict_of_samples['sample']:
print(dict_of_samples['sample'][index].keys())
#print(dict_of_samples['sample'][index])
#sys.exit()
#"sample_collection_project_name":"sample_collection_project_name"
sample_project_table_id =""
if "sample_plan_name" in dict_of_samples['sample'][index].keys() or "sample_plan_ID" in dict_of_samples['sample'][index].keys() or "sample_collection_project_name" in dict_of_samples['sample'][index].keys() :
#sample_plan_fields = {};
if "sample_collection_project_name" in dict_of_samples['sample'][index].keys():
sample_project_table_id = check_exists_id(dict_of_samples['sample'][index]["sample_collection_project_name"],"sample_collection_project_name",'projects')
#sample_plan_fields['sample_plan_name'] = dict_of_samples['sample'][index]["sample_plan_name"]
elif "sample_plan_name" in dict_of_samples['sample'][index].keys():
sample_project_table_id = check_exists_id(dict_of_samples['sample'][index]["sample_plan_name"],"sample_plan_name",'projects')
#sample_project_table_id = sample_project_table_id [0]
else:
sample_project_table_id = check_exists_id(dict_of_samples['sample'][index]["sample_plan_ID"],"sample_plan_ID",'projects')
#sample_project_table_id = sample_project_table_id [0]
# sample_plan_fields['sample_plan_ID'] = dict_of_samples['sample'][index]["sample_plan_ID"]
if not sample_project_table_id:
print("doesnt exist")
sample_project_table_id =create_insert(dict_of_samples['sample'][index],{'sample_plan_name':'sample_plan_name','sample_collection_project_name':'project_name','sample_plan_ID':'sample_plan_id'},"","projects",3)
#sample_project_table_id = sample_project_table_id [0]
dict_of_samples['sample'][index]['sample_plan_table_id'] = sample_project_table_id[0]
#sys.exit()
print("is it here?")
dict_sample_table = dict_of_samples['sample'][index]
sample_table_fields = {"sample_collector_sample_id":dict_of_samples['sample'][index]["sample_collector_sample_ID"]}
if dict_of_samples['sample'][index]["sample_collector_sample_ID"] in sample_flagged_list:
sample_table_fields["validation_status"]= "flagged"
else:
sample_table_fields["validation_status"]= "curated"
if 'sample_plan_table_id' in dict_of_samples['sample'][index].keys():
sample_table_fields["project_id"]=dict_of_samples['sample'][index]['sample_plan_table_id']
else:
sample_table_fields["project_id"] = None
#if 'sample_plan_table_id' in dict_of_samples['sample'][index].keys():
# sample_table_fields["sample_plan_table_id"]=dict_of_samples['sample'][index]["sample_plan_table_id"]
#sample_table_fields[keys]=keys
print ("here")
sample_id = check_exists_id(dict_of_samples['sample'][index]["sample_collector_sample_ID"],"sample_collector_sample_id","samples")
if not sample_id:
print ("doesnt exists")
print (dict_sample_table)
print (sample_table_fields)
sample_id =create_insert(sample_table_fields,{"sample_collector_sample_id":"sample_collector_sample_id","validation_status":"validation_status","project_id":"project_id"},"","samples",3)
#sys.exit()
sample_id = sample_id[0]
dict_of_samples['sample'][index]["sample_id"] = sample_id
#print ( 'inicio',sample_id,dict_of_samples['sample'][index]["sample_id"])
#sys.exit()
# sample_table_id =create_insert(dict_of_samples['sample'][index],{"sample_collector_contact_name":"contact_name","sample_collected_by_laboratory_name":"laboratory_name","sample_collector_contact_email":"contact_email"},"","contact_information",3)
print ("here samples")
#sys.exit()
#alt_id =""
if ("alternative_sample_ID") in dict_of_samples['sample'][index].keys():
dict_of_samples['sample'][index]["alternative_sample_ID"] = str(dict_of_samples['sample'][index]["alternative_sample_ID"])
list_alt_ids =[]
if ("|" in dict_of_samples['sample'][index]["alternative_sample_ID"]):
list_alt = re.split("|",dict_of_samples['sample'][index]["alternative_sample_ID"])
for alt in list_alt:
alt_id = check_exists_id([sample_id,alt],["sample_id","alternative_sample_id"],"alternative_sample_ids")
if alt_id != "yes":
alt_id =create_insert({"alternative_sample_id":alt,"sample_id":sample_id},{"alternative_sample_id":"alternative_sample_id","sample_id":"sample_id","note":"note"},"","alternative_sample_ids",3)
list_alt_ids.append(alt_id)
elif (";" in dict_of_samples['sample'][index]["alternative_sample_ID"]):
list_alt = re.split(";",dict_of_samples['sample'][index]["alternative_sample_ID"])
for alt in list_alt:
alt_id = check_exists_id([sample_id,alt],["sample_id","alternative_sample_id"],"alternative_sample_ids")
if alt_id != "yes":
alt_id =create_insert({"alternative_sample_id":alt,"sample_id":sample_id},{"alternative_sample_id":"alternative_sample_id","sample_id":"sample_id","note":"note"},"","alternative_sample_ids",3)
list_alt_ids.append(alt_id)
elif ("," in dict_of_samples['sample'][index]["alternative_sample_ID"]):
list_alt = re.split(",",dict_of_samples['sample'][index]["alternative_sample_ID"])
for alt in list_alt:
alt_id = check_exists_id([sample_id,alt],["sample_id","alternative_sample_id"],"alternative_sample_ids")
if alt_id != "yes":
alt_id =create_insert({"alternative_sample_id":alt,"sample_id":sample_id},{"alternative_sample_id":"alternative_sample_id","sample_id":"sample_id","note":"note"},"","alternative_sample_ids",3)
list_alt_ids.append(alt_id)
else:
alt = dict_of_samples['sample'][index]["alternative_sample_ID"]
alt_id = check_exists_id([sample_id,alt],["sample_id","alternative_sample_id"],"alternative_sample_ids")
if alt_id != "yes":
alt_id =create_insert({"alternative_sample_id":alt,"sample_id":sample_id},{"alternative_sample_id":"alternative_sample_id","sample_id":"sample_id","note":"note"},"","alternative_sample_ids",3)
list_alt_ids.append(alt_id)
else:
sample_table_fields["alternative_sample_id"]=None
#sys.exit()
contact_info_id=""
if "sample_collector_contact_name" in dict_of_samples['sample'][index].keys():
contact_info_id = check_exists_id(dict_of_samples['sample'][index]["sample_collector_contact_name"],"contact_name","contact_information")
print ("done checking")
if not contact_info_id:
print ("doesnt exists")
contact_info_id =create_insert(dict_of_samples['sample'][index],{"sample_collector_contact_name":"contact_name","sample_collected_by_laboratory_name":"laboratory_name","sample_collector_contact_email":"contact_email","note":"note"},"","contact_information",4)
#contact_info_id = contact_info_id[0]
else:
print (contact_info_id,"exists")
contact_info_id = contact_info_id[0]
print ("done alternative_ids")
#sys.exit()
if contact_info_id:
dict_of_samples['sample'][index]["contact_information"] = contact_info_id
else:
dict_of_samples['sample'][index]["contact_information"] = None
# print (contact_info_id, " contact info")
print ("testing", sample_id,dict_of_samples['sample'][index]["sample_id"],dict_of_samples['sample'][index]["contact_information"] )
collection_fields = {"sample_id":"sample_id","sample_collected_by":"sample_collected_by","contact_information":"contact_information",
"sample_collection_date":"sample_collection_date","sample_collection_date_precision":"sample_collection_date_precision", "presampling_activity_details":"presampling_activity_details",
"sample_received_date":"sample_received_date","original_sample_description":"original_sample_description","specimen_processing":"specimen_processing","sample_storage_method":"sample_storage_method","sample_storage_medium":"sample_storage_medium",
"collection_device":"collection_device","collection_method":"collection_method"}
collection_controlled = {"sample_collected_by":["ontology_terms","ontology_id"],"sample_collection_date_precision":["ontology_terms","ontology_id"],"specimen_processing":["ontology_terms","ontology_id"],"collection_device":["ontology_terms","ontology_id"],"collection_method":["ontology_terms","ontology_id"]}
collection_id = check_exists_id(dict_of_samples['sample'][index]["sample_id"],"sample_id","collection_information")
if not collection_id:
print ("doesnt exists")
collection_id =create_insert(dict_of_samples['sample'][index],collection_fields,collection_controlled,"collection_information",len(collection_fields))
else:
print (collection_id,"exists")
print (collection_id[0],"ready")
#sys.exit()
collection_id = collection_id[0]
dict_of_samples['sample'][index]["collection_information"] = collection_id
if "purpose_of_sampling" in dict_of_samples['sample'][index].keys():
print ("trying to check")
spurposes = dict_of_samples['sample'][index]["purpose_of_sampling"]
# print (spurposes)
for purpose in spurposes:
purpose_sampling_id = check_exists_id([collection_id,purpose],["id","term_id","ontology_terms","ontology_id"],"sample_purposes")
if purpose_sampling_id != "yes":
print ("doesnt exists")
print(collection_id,purpose, "here you after doesnt")
purpose_sampling_id =create_insert({"id":collection_id,"term_id":purpose},{"id":"id","term_id":"term_id"},{"term_id":["ontology_terms","ontology_id"]},"sample_purposes",2)
else:
print (purpose_sampling_id,"exists")
#sys.exit()
if "presampling_activity" in dict_of_samples['sample'][index].keys():
print ("trying to check")
sactivities = dict_of_samples['sample'][index]["presampling_activity"]
print(sactivities)
#sys.exit()
# print (spurposes)
for activity in sactivities:
psampling_activity_id = check_exists_id([collection_id,activity],["id","term_id","ontology_terms","ontology_id"],"sample_activity")
if psampling_activity_id != "yes":
print ("doesnt exists")
psampling_activity_id =create_insert({"id":collection_id,"term_id":activity},{"id":"id","term_id":"term_id"},{"term_id":["ontology_terms","ontology_id"]},"sample_activity",2)
else:
print (psampling_activity_id,"exists")
if "geo_loc_name (site)" in dict_of_samples['sample'][index].keys():
geo_loc_site_id = check_exists_id(dict_of_samples['sample'][index]["geo_loc_name (site)"],"geo_loc_name_site","geo_loc_name_sites")
if not geo_loc_site_id:
print ("doesnt exists")
geo_loc_site_id =create_insert(dict_of_samples['sample'][index],{"geo_loc_name (site)":"geo_loc_name_site" },"","geo_loc_name_sites",1)
else:
print (geo_loc_site_id,"exists")
dict_of_samples['sample'][index]["geo_loc_name_site_id"] = geo_loc_site_id[0]
else:
dict_of_samples['sample'][index]["geo_loc_name_site_id"] = None
geo_loc_fields = {"sample_id":"sample_id","geo_loc_name (country)":"country","geo_loc_name (state/province/region)":"state_province_region","geo_loc_name_site_id":"site","geo_loc latitude":"latitude","geo_loc longitude":"longitude"}
geo_loc_controlled={"geo_loc_name (country)":["countries","ontology_id"],"geo_loc_name (state/province/region)":["state_province_regions","ontology_id"]}
geo_loc_id = check_exists_id(dict_of_samples['sample'][index]["sample_id"],"sample_id","geo_loc")
if not geo_loc_id:
print ("doesnt exists")
geo_loc_id =create_insert(dict_of_samples['sample'][index],geo_loc_fields,geo_loc_controlled,"geo_loc",len(geo_loc_fields))
else:
print (geo_loc_id,"exists")
#sys.exit()
food_data_fields = {"sample_id":"sample_id","food_product_production_stream":"food_product_production_stream","food_product_origin geo_loc (country)":"food_product_origin_country","food_packaging_date":"food_packaging_date","food_quality_date":"food_quality_date"}
food_controlled = {"food_product_production_stream":["ontology_terms","ontology_id"],"food_product_origin geo_loc (country)":["countries","ontology_id"]}
food_data_id = check_exists_id(dict_of_samples['sample'][index]["sample_id"],"sample_id","food_data")
if not food_data_id:
print ("doesnt exists")
food_data_id =create_insert(dict_of_samples['sample'][index],food_data_fields,food_controlled,"food_data",len(food_data_fields))
else:
print (food_data_id,"exists")
food_data_id = food_data_id[0]
#sys.exit()
multi(dict_of_samples['sample'][index],"food_product","food_data",food_data_id,"food_data_product")
#sys.exit()
multi(dict_of_samples['sample'][index],"food_product_properties","food_data",food_data_id,"food_data_product_property")
multi(dict_of_samples['sample'][index],"animal_source_of_food","food_data",food_data_id,"food_data_source")
multi(dict_of_samples['sample'][index],"food_packaging","food_data",food_data_id,"food_data_packaging")
anatomical_data_fields = {"sample_id":"sample_id","anatomical_region":"anatomical_region"}
anatomical_controlled = {"anatomical_region":["ontology_terms","ontology_id"]}
anatomical_data_id = check_exists_id(dict_of_samples['sample'][index]["sample_id"],"sample_id","anatomical_data")
if not anatomical_data_id:
print ("doesnt exists")
anatomical_data_id =create_insert(dict_of_samples['sample'][index],anatomical_data_fields,anatomical_controlled,"anatomical_data",len(anatomical_data_fields))
else:
print (anatomical_data_id,"exists")
anatomical_data_id= anatomical_data_id[0]
multi(dict_of_samples['sample'][index],"body_product","anatomical_data",anatomical_data_id,"anatomical_data_body")
multi(dict_of_samples['sample'][index],"anatomical_part","anatomical_data",anatomical_data_id,"anatomical_data_part")
multi(dict_of_samples['sample'][index],"anatomical_material","anatomical_data",anatomical_data_id,"anatomical_data_material")
environmental_data_fields = {"sample_id":"sample_id","air_temperature":"air_temperature","air_temperature_units":"air_temperature_units","water_temperature_units":"water_temperature_units",
"sediment_depth_units":"sediment_depth_units","water_depth_units":"water_depth_units",
"sediment_depth":"sediment_depth","water_depth":"water_depth","water_temperature":"water_temperature","available_data_type_details":"available_data_type_details"}
environmental_controlled = {"air_temperature_units":["ontology_terms","ontology_id"],"water_temperature_units":["ontology_terms","ontology_id"],"sediment_depth_units":["ontology_terms","ontology_id"],"air_temperature_units":["water_depth_units","ontology_id"]}
if (dict_of_samples['environment']):
for indexes in dict_of_samples['environment']:
if dict_of_samples['environment'][indexes]['sample_collector_sample_ID'] == dict_of_samples['sample'][index]['sample_collector_sample_ID']:
for fields_env in dict_of_samples['environment'][indexes]:
if fields_env != dict_of_samples['sample'][index].keys():
dict_of_samples['sample'][index][fields_env] = dict_of_samples['environment'][indexes][fields_env]
environmental_data_id = check_exists_id(dict_of_samples['sample'][index]["sample_id"],"sample_id","environmental_data")
if not environmental_data_id:
print ("doesnt exists")
environmental_data_id =create_insert(dict_of_samples['sample'][index],environmental_data_fields,environmental_controlled,"environmental_data",len(environmental_data_fields))
else:
print (environmental_data_id,"exists")
environmental_data_id= environmental_data_id[0]
multi(dict_of_samples['sample'][index],"weather_type","environmental_data",environmental_data_id,"environmental_data_weather_type")
multi(dict_of_samples['sample'][index],"presampling_weather_conditions","environmental_data",environmental_data_id,"environmental_data_presampling_weather_conditions")
multi(dict_of_samples['sample'][index],"envrionmental_material","environmental_data",environmental_data_id,"environmental_data_material")
multi(dict_of_samples['sample'][index],"environmental_site","environmental_data",environmental_data_id,"environmental_data_site")
multi(dict_of_samples['sample'][index],"available_data_types","environmental_data",environmental_data_id,"environmental_data_available_data_type")
print("DONE???")
multi(dict_of_samples['sample'][index],"animal_or_plant_population","environmental_data",environmental_data_id,"environmental_data_animal_plant")
print ('DONE_POPULATION')
if "host_origin geo_loc (country)" in dict_of_samples['sample'][index].keys():
print ("STARTING HOSTCOUNTYR")
host_country[dict_of_samples['sample'][index][sample_id]] = dict_of_samples['sample'][index]["host_origin geo_loc (country)"]
print ("DONE HCOUNTRY")
print (dict_of_samples['host'])
for index in dict_of_samples['host']:
print (dict_of_samples['host'][index])
if "host (breed)" in dict_of_samples['host'][index].keys():
host_breed_id = check_exists_id(dict_of_samples['host'][index]["host (breed)"],"host_breed","host_breeds")
if not host_breed_id:
print ("doesnt exists")
host_breed_id =create_insert(dict_of_samples['host'][index],{"host (breed)":"host_breed" },"","host_breeds",1)
else:
print (host_breed_id,"exists")
dict_of_samples['host'][index]["host_breed_id"] = host_breed_id[0]
else:
dict_of_samples['host'][index]["geo_loc_name_site_id"] = None
if "host_disease" in dict_of_samples['host'][index].keys():
host_disease_id = check_exists_id(dict_of_samples['host'][index]["host_disease"],"host_disease","host_diseases")
if not host_disease_id:
print ("doesnt exists")
host_disease_id =create_insert(dict_of_samples['host'][index],{"host_disease":"host_disease" },"","host_diseases",1)
else:
print (host_disease_id,"exists")
dict_of_samples['host'][index]["host_disease_id"] = host_disease_id[0]
else:
dict_of_samples['host'][index]["geo_loc_name_site_id"] = None
print('failed_here?')
sample_id = check_exists_id(dict_of_samples['sample'][index]["sample_collector_sample_ID"],"sample_collector_sample_id","samples")
print ('maybe_not')
sample_id = sample_id[0]
#print (host_country)
#if host_country:
if sample_id in host_country.keys():
dict_of_samples['sample'][index]["host_origin geo_loc (country)"] = host_country[sample_id]
dict_of_samples['host'][index]["sample_id"] = sample_id
organism_key=""
if ("host (common name)" in dict_of_samples['host'][index].keys()):
organism_key = "host (common name)"
elif ("host (scientific name)" in dict_of_samples['host'][index].keys()):
organism_key = "host (scientific name)"
host_fields = {"sample_id":"sample_id",organism_key:"host_organism","host (food production name)":"host_food_production_name","host_origin geo_loc (country)":"host_origin_geo_loc_name_country","host (ecotype)":"host_ecotype","host_disease_id":"host_disease","host_breed_id":"host_breed","host_age_bin":"host_age_bin"}
host_controlled = {organism_key:["host_organisms","ontology_id"],"host (food production name)":["ontology_terms","ontology_id"],"host_origin geo_loc (country)":["countries","ontology_id"],"host_age_bin":["ontology_terms","ontology_id"]}
host_id = check_exists_id(dict_of_samples['host'][index]["sample_id"],"sample_id","hosts")
if not host_id:
print ("doesnt exists")
host_id =create_insert(dict_of_samples['host'][index],host_fields,host_controlled,"hosts",len(host_fields))
else:
print (host_id,"exists")
print ("FINISHED HOST")
#sys.exit()
for index in dict_of_samples['isolate']:
print(dict_of_samples['isolate'][index],"OLHA O ERRO AQUI MANE")
isolate_id = ""
if "isolate_ID" in dict_of_samples['isolate'][index].keys():
sample_id = check_exists_id(dict_of_samples['isolate'][index]["sample_collector_sample_ID"],"sample_collector_sample_id","samples")
sample_id = sample_id[0]
dict_of_samples['isolate'][index]["sample_id"] = sample_id
print(dict_of_samples['isolate'][index])
if "strain" in dict_of_samples['isolate'][index].keys():
strain_id = check_exists_id(dict_of_samples['isolate'][index]["strain"],"strain","strains")
if not strain_id:
print ("doesnt exists")
strain_id =create_insert(dict_of_samples['isolate'][index],{"strain":"strain" },"","strains",1)
else:
print (strain_id,"exists")
dict_of_samples['isolate'][index]["strain_id"] = strain_id[0]
else:
dict_of_samples['isolate'][index]["strain_id"] = None
contact_info_id =""
if "isolated_by_contact_name" in dict_of_samples['isolate'][index].keys():
contact_info_id = check_exists_id(dict_of_samples['isolate'][index]["isolated_by_contact_name"],"contact_name","contact_information")
print ("done checking")
if not contact_info_id:
print ("doesnt exists")
contact_info_id =create_insert(dict_of_samples['isolate'][index],{"isolated_by_contact_name":"contact_name","isolated_by_laboratory_name":"laboratory_name","isolated_by_contact_email":"contact_email"},"","contact_information",3)
else:
print (contact_info_id,"exists")
contact_info_id = contact_info_id[0]
if contact_info_id:
dict_of_samples['isolate'][index]["contact_information"] = contact_info_id
print (contact_info_id, " contact info")
else:
dict_of_samples['isolate'][index]["contact_information"] = None
isolate_fields = {"sample_id":"sample_id","isolate_ID":"isolate_id","strain_id":"strain","microbiological_method":"microbiological_method","progeny_isolate_id":"progeny_isolate_id","IRIDA_isolate_ID":"irida_sample_id","IRIDA_project_ID":"irida_project_id","biosample_accession":"biosample_id","bioproject_accession":"bioproject_id","isolated_by":"isolated_by","contact_information":"contact_information","isolation_date":"isolation_date","isolate_received_date":"isolate_received_date","organism":"organism","taxonomic_identification_process":"taxonomic_identification_process","serovar":"serovar","serotyping_method":"serotyping_method","phagetype":"phagetype"}
isolate_controlled = {"isolated_by":["ontology_terms","ontology_id"],"organism":["microbes","ontology_id"],"taxonomic_identification_process":["ontology_terms","ontology_id"]}
isolate_id = check_exists_id(dict_of_samples['isolate'][index]["isolate_ID"],"isolate_id","isolates")
if not isolate_id:
print ("doesnt exists")
isolate_id =create_insert(dict_of_samples['isolate'][index],isolate_fields,isolate_controlled,"isolates",len(isolate_fields))
else:
print (isolate_id,"exists")
isolate_id= isolate_id[0]
# if ( dict_of_samples['isolate'][index]['isolate_ID'] == "CC-MBS0564R"):
## print (dict_of_samples['isolate'][index])
# print(isolate_id)
# sys.exit()
if ("alternative_isolate_ID") in dict_of_samples['isolate'][index].keys():
list_alt_ids =[]
dict_of_samples['isolate'][index]["alternative_isolate_ID"] = str(dict_of_samples['isolate'][index]["alternative_isolate_ID"])
if ("|" in dict_of_samples['isolate'][index]["alternative_isolate_ID"]):
list_alt = dict_of_samples['isolate'][index]["alternative_isolate_ID"].split("|")
print (list_alt)
for alt in list_alt:
alt = alt.strip()
alt_id = check_exists_id([isolate_id,alt],["isolate_id","alternative_isolate_ID"],"alternative_isolate_ids")
if alt_id != "yes":
alt_id =create_insert({"alternative_isolate_ID":alt,"isolate_id":isolate_id},{"alternative_isolate_ID":"alternative_isolate_id","isolate_id":"isolate_id","note":"note"},"","alternative_isolate_ids",3)
list_alt_ids.append(alt_id)
elif (";" in dict_of_samples['isolate'][index]["alternative_isolate_ID"]):
list_alt = dict_of_samples['isolate'][index]["alternative_isolate_ID"].split(";")
for alt in list_alt:
alt_id = check_exists_id([isolate_id,alt],["isolate_id","alternative_isolate_ID"],"alternative_isolate_ids")
if alt_id != "yes":
alt_id =create_insert({"alternative_isolate_ID":alt,"isolate_id":isolate_id},{"alternative_isolate_ID":"alternative_isolate_id","isolate_id":"isolate_id","note":"note"},"","alternative_isolate_ids",3)
list_alt_ids.append(alt_id)
elif ("," in dict_of_samples['isolate'][index]["alternative_isolate_ID"]):
list_alt = dict_of_samples['isolate'][index]["alternative_isolate_ID"].split(",")
for alt in list_alt:
alt_id = check_exists_id([isolate_id,alt],["isolate_id","alternative_isolate_ID"],"alternative_isolate_ids")
if alt_id != "yes":
alt_id =create_insert({"alternative_isolate_ID":alt,"isolate_id":isolate_id},{"alternative_isolate_ID":"alternative_isolate_id","isolate_id":"isolate_id","note":"note"},"","alternative_isolate_ids",3)
list_alt_ids.append(alt_id)
else:
alt = dict_of_samples['isolate'][index]["alternative_isolate_ID"]
alt_id = check_exists_id([isolate_id,alt],["isolate_id","alternative_isolate_ID"],"alternative_isolate_ids")
if alt_id != "yes":
alt_id =create_insert({"alternative_isolate_ID":alt,"isolate_id":isolate_id},{"alternative_isolate_ID":"alternative_isolate_id","isolate_id":"isolate_id","note":"note"},"","alternative_isolate_ids",3)
list_alt_ids.append(alt_id)
else:
sample_table_fields["alternative_isolate_id"]=None
# sys.exit()
if (dict_of_samples['risk']):
for index in dict_of_samples['risk']:
print("died risk")
sample_id = check_exists_id(dict_of_samples['risk'][index]["sample_collector_sample_ID"],"sample_collector_sample_id","samples")
sample_id = sample_id[0]
dict_of_samples['risk'][index]["sample_id"] = sample_id
isolate_id= None
risk_id=""
if ("isolate_ID" in dict_of_samples['risk'][index].keys() ):
isolate_id = check_exists_id(dict_of_samples['risk'][index]["isolate_ID"],"isolate_id","isolates")
isolate_id = isolate_id[0]
dict_of_samples['risk'][index]["isolate_id"] = isolate_id
risk_id=check_exists_id(dict_of_samples['risk'][index]["isolate_id"],"isolate_id","risk_assessment")
else:
risk_id=check_exists_id(dict_of_samples['risk'][index]["sample_id"],"sample_id","risk_assessment")
risk_fields = {"sample_id":"sample_id","isolate_id":"isolate_id","sequence_ID":"sequence_id","prevalence_metrics":"prevalence_metrics","prevalence_metrics_details":"prevalence_metrics_details","stage_of_production":"stage_of_production","experimental_intervention_details":"experimental_intervention_details"}
risk_controlled = {"stage_of_production":["ontology_terms","ontology_id"]}
#risk_id = check_exists_id(dict_of_samples['publicRep'][index]["sample_id"],"sample_id","public_repository_information]")
if not risk_id:
print ("doesnt exists")
risk_id =create_insert(dict_of_samples['risk'][index],risk_fields,risk_controlled,"risk_assessment",len(risk_fields))
else:
print (risk_id,"exists")
if "experimental_intervention" in dict_of_samples['risk'][index].keys():
print ("trying to check")
sactivities = dict_of_samples['risk'][index]["experimental_intervention"]
# print (spurposes)
for activity in sactivities:
psampling_activity_id = check_exists_id([risk_id,activity],["id","term_id","ontology_terms","ontology_id"],"risk_activity")
if psampling_activity_id != "yes":
print ("doesnt exists")
psampling_activity_id =create_insert({"id":risk_id,"term_id":activity},{"id":"id","term_id":"term_id"},{"term_id":["ontology_terms","ontology_id"]},"risk_activity",2)
else:
print (psampling_activity_id,"exists")
#print(dict_of_samples['AMR'][0])
# print (len(dict_of_samples['AMR']),"tamanho total")
#sys.exit()
print ("DONE RISK")
#rint (dict_of_samples['extractions'])
#sys.exit()
for index in dict_of_samples['extractions']:
flag_continue =0
if (mode == 1):
if 'isolate_ID' in dict_of_samples['extractions'][index].keys():
isolate_id = check_exists_id(dict_of_samples['extractions'][index]["isolate_ID"],"isolate_id","isolates")
isolate_id = isolate_id[0]
wgs_id = check_exists_id(isolate_id,"isolate_id","wgs_extractions")
if not wgs_id:
extraction_id = extraction_insert(dict_of_samples['extractions'][index])
create_insert({"isolate_id":isolate_id,"extraction_id":extraction_id[0]},{"isolate_id":"isolate_id","extraction_id":"extraction_id"},"","wgs_extractions",2)
flag_continue=1
else:
if 'sample_collector_sample_ID' in dict_of_samples['extractions'][index].keys():
sample_id = check_exists_id(dict_of_samples['extractions'][index]["sample_collector_sample_ID"],"sample_collector_sample_id","samples")
sample_id = sample_id[0]
metagenomics_id = check_exists_id(sample_id,"sample_id","wgs_extractions")
if not metagenomics_id:
extraction_id = extraction_insert(dict_of_samples['extractions'][index])
create_insert({"sample_id":sample_id,"extraction_id":extraction_id[0]},{"sample_id":"sample_id","extraction_id":"extraction_id"},"","metagenomic_extractions",2)
flag_continue = 1
##sequneces
for index in dict_of_samples['sequence']:
#print (dict_of_samples['sequence'][index])
#sys.exit()
print("died sequence")
flag_continue =0
extraction_id=""
if (mode == 1):
if 'isolate_ID' in dict_of_samples['sequence'][index].keys():
isolate_id = check_exists_id(dict_of_samples['sequence'][index]["isolate_ID"],"isolate_id","isolates")
isolate_id = isolate_id[0]
extraction_id = check_exists_id(isolate_id,"isolate_id","wgs_extractions")
flag_continue = 1
else:
if 'sample_collector_sample_ID' in dict_of_samples['sequence'][index].keys():
sample_id = check_exists_id(dict_of_samples['sequence'][index]["sample_collector_sample_ID"],"sample_collector_sample_id","samples")
sample_id = sample_id[0]
extraction_id = check_exists_id(sample_id,"sample_id","metagenomic_extractions")
flag_continue = 1
contact_info_id =""
if flag_continue == 1:
if "sequenced_by_contact_name" in dict_of_samples['sequence'][index].keys():
contact_info_id = check_exists_id(dict_of_samples['sequence'][index]["sequenced_by_contact_name"],"contact_name","contact_information")
print ("done checking")
if not contact_info_id:
print ("doesnt exists")
contact_info_id =create_insert(dict_of_samples['sequence'][index],{"sequenced_by_contact_name":"contact_name","sequenced_by_laboratory_name":"laboratory_name","sequenced_by_contact_email":"contact_email"},"","contact_information",3)
else:
print (contact_info_id,"exists")
contact_info_id = contact_info_id[0]
if contact_info_id:
dict_of_samples['sequence'][index]["contact_information"] = contact_info_id
print (contact_info_id, " contact info")
else:
dict_of_samples['sequence'][index]["contact_information"] = None
"""CREATE TABLE SEQUENCING (
id INT GENERATED ALWAYS AS IDENTITY PRIMARY KEY,
SAMPLE_ID INTEGER REFERENCES SAMPLES(id),
ISOLATE_ID INTEGER REFERENCES ISOLATES(id),
LIBRARY_ID TEXT,
CONTACT_INFORMATION INTEGER REFERENCES CONTACT_INFORMATION(id),
SEQUENCED_BY INTEGER REFERENCES AGENCIES(id),
SEQUENCING_PROJECT_NAME TEXT,
SEQUENCING_PLATFORM INTEGER REFERENCES SEQUENCING_PLATFORMS(id),
SEQUENCING_INSTRUMENT INTEGER REFERENCES SEQUENCING_INSTRUMENTS(id),
LIBRARY_PREPARATION_KIT TEXT,
SEQUENCING_PROTOCOL TEXT,
R1_FASTQ_FILENAME TEXT,
R2_FASTQ_FILENAME TEXT,
FAST5_FILENAME TEXT,
ASSEMBLY_FILENAME TEXT
"""
print (extraction_id,'Acho que ferra ai', mode, '\n')
dict_of_samples['sequence'][index]["extraction_id"]= extraction_id[0]
print ("talvez aqui?")
sequence_fields = {"extraction_id":"extraction_id","sequenced_by":"sequenced_by","contact_information":"contact_information","library_ID":"library_id","sequencing_project_name":"sequencing_project_name",
"assembly_filename":"genome_sequence_filename","sequencing_platform":"sequencing_platform","sequencing_instrument":"sequencing_instrument",
"library_preparation_kit":"library_preparation_kit","sequencing_protocol":"sequencing_protocol","r1_fastq_filename":"r1_fastq_filename","r2_fastq_filename":"r2_fastq_filename",
"fast5_filename":"fast5_filename","sequencing_assay_type":"sequencing_assay_type","dna_fragment_length":"dna_fragment_length",
"genomic_target_enrichment_method":"genomic_target_enrichment_method",
"genomic_target_enrichment_method_details":"genomic_target_enrichment_method_details",
"amplicon_pcr_primer_scheme":"amplicon_pcr_primer_scheme",
"amplicon_size":"amplicon_size",
"sequencing_flow_cell_version":"sequencing_flow_cell_version"}
sequence_controlled = {"sequenced_by":["ontology_terms","ontology_id"],
"sequencing_platform":["ontology_terms","ontology_id"],
"sequencing_instrument":["ontology_terms","ontology_id"],
"sequencing_assay_type" :["ontology_terms","ontology_id"],
"genomic_target_enrichment_method":["ontology_terms","ontology_id"]
}
print ("talvez aqui?")
sequence_id=check_exists_id(dict_of_samples['sequence'][index]["extraction_id"],"extraction_id","sequencing")
print ('PASSED HERE FIRST CHEQUING SEQUENCE')
if not sequence_id:
print ("doesnt exists")
sequence_id =create_insert(dict_of_samples['sequence'][index],sequence_fields,sequence_controlled,"sequencing",len(sequence_fields))
else:
print (sequence_id,"exists")
sequence_id = sequence_id[0]
if "purpose_of_sequencing" in dict_of_samples['sequence'][index].keys():
print ("trying to check")
spurposes = dict_of_samples['sequence'][index]["purpose_of_sequencing"]
# print (spurposes)
for purpose in spurposes:
purpose_of_sequencing_id = check_exists_id([sequence_id,purpose],["id","term_id","ontology_terms","ontology_id"],"sequencing_purposes")
print (purpose_of_sequencing_id)
if purpose_of_sequencing_id != "yes":
print ("doesnt exists")
purpose_of_sequencing_id =create_insert({"id":sequence_id,"term_id":purpose},{"id":"id","term_id":"term_id"},{"term_id":["ontology_terms","ontology_id"]},"sequencing_purposes",2)
else:
print (purpose_of_sequencing_id,"exists")
for index in dict_of_samples['bioinformatics']:
reg_keys = [
"sample_collector_sample_ID",
"alternative_sample_ID",
"isolate_ID",
"alternative_isolate_ID"
]
extra_keys = [key for key in dict_of_samples['bioinformatics'][index].keys() if key not in reg_keys]
if extra_keys:
if (mode == 1):
isolate_id = check_exists_id(dict_of_samples['bioinformatics'][index]["isolate_ID"],"isolate_id","isolates")
isolate_id = isolate_id[0]
extraction_id = check_exists_id(isolate_id,"isolate_id","wgs_extractions")
sequence_id = check_exists_id(extraction_id[0],"extraction_id","sequencing")
dict_of_samples['bioinformatics'][index]["sequencing_id"] = sequence_id[0]
else:
sample_id = check_exists_id(dict_of_samples['bioinformatics'][index]["sample_collector_sample_ID"],"sample_collector_sample_id","samples")
sample_id = sample_id[0]
extraction_id = check_exists_id(sample_id,"isolate_id","wgs_extractions")